Choosing the Right Electronic Lab Notebook

Contributing editor Tanuja Koppal, PhD, talks to two chemists, who are both users of electronic lab notebooks (ELNs), about their experiences and what they’ve learned. They discuss the reasons behind transitioning from a paper notebook to an ELN, what factors they considered important to have in an ELN, how they went about choosing the right vendor, and how they implemented the ELN to suit their needs.

M. Emilia Di Francesco obtained her master’s degree in chemistry from the University of Rome La Sapienza, and soon after joined the Merck Research Laboratories, working as a medicinal chemist in both their Italian and UK research sites. After a few years, she moved to Cambridge, UK, for her PhD studies, and then returned to Merck (Rome, Italy, and Boston, Massachusetts, USA), where she led medicinal chemistry projects in several different therapeutic areas, including antiviral and oncology. In 2012, she joined the MD Anderson Cancer Center, Houston, Texas, USA, as the group leader for the medicinal chemistry team in the newly founded Institute for Applied Cancer Science (IACS). Together with the team at IACS, she is focusing on metabolism and epigenetic targets and leveraging the clinical and basic research expertise at MD Anderson, with the goal of developing novel therapies for cancer patients.

Excerpts from an interview with M. Emilia Di Francesco, PhD, group leader for Medicinal Chemistry at the Institute for Applied Cancer Science (IACS) at MD Anderson Cancer Center

Q: As a medicinal chemist, why do you need ELNs for your work?

A: Currently we use ELNs to track the experimental procedures used for chemical synthesis as well as for analytical characterization of the quality and purity of the end product. I first came in contact with ELNs while working at Merck, and like many big pharma, they transitioned to using ELNs many years ago for all the advantages it offered. So when it was time to move out of big pharma, I wanted to invest in and implement ELNs in the lab, although I was moving into an organization with a much smaller operation.

Q: Can you mention some of the advantages that ELNs offer you?

A: On a daily basis ELNs simplify the overall operations in terms of detailing experimental procedures, and you can preselect certain features, so that the regular maintenance becomes quick and routine. Beyond that, ELNs offer a way to share procedures and knowledge across the team. Within a drug discovery organization, you have chemists, biologists, and pharmacologists, and the features of the ELN can be tweaked so that it fits everyone’s needs. With ELNs, you have the ability to access the primary data generated by other labs on the team, which is very useful. It’s a fantastic tool not only to collect text and procedures but also to collect primary data in multiple formats. For instance, I can import imaging data that a biologist generates, along with the NMR spectra from my chemistry group and other types of data, in a PDF or in Excel sheets. I can work on my notebook off-line and synchronize it later.

Q: Do ELNs offer any particular advantages for a chemist?

A: For chemists, the ELN offers a chemical structure drawing interface that affords a clear understanding of the chemical reaction taking place. There is also access to a small, searchable database of widely used commercial reagents that can be added to your notebook, which eliminates the need to draw it. The ELN is also searchable for text, and you can search by chemical structure or reaction. It’s easy to set up an experiment in your notebook and it’s much easier for everyone to then read and duplicate it. When it comes time to upload your data into a publication or patent, it’s easy to export the information, whether into a Word document or any other format. For patentability, all notebook entries must be complete with a time stamp and must be countersigned by someone knowledgeable in the lab. The time stamp is an automatic feature of the ELN, and it helps us all track and stay within the time frame of our projects. What I hated most about lab notebooks was creating the index, where I had to enter the experiment and yields manually. In ELNs, the index is an automatic feature of the software.

Q: Is the interface simple and user-friendly?

A: The interface is a single page of the notebook and you can work your way up to see the data entered by you and your colleagues across teams. Every change is recorded and makes its way into the history of the page. A page is closed when all ancillary data has been included and has been signed and countersigned by a witness. It is then sent to the long-term archive on the server. However, the data can always be accessed and modified, if needed. We have a secure server and hence, data security is not a concern. We have set up our ELN as an open-access system in order to share knowledge and access all the primary data. With open access, we can get to the primary data even after a colleague has left the company, which makes it easier for publishing a paper or patent. It’s also highly customizable.

Q: What features would you like to see added to it?

A: The ELN we had at Merck had a lot more bells and whistles, some of which I do miss, but it’s all a matter of having the budget to make the investment. For instance, at Merck every piece of analytical data that was sent to the printer was also saved as a PDF and could be directly imported into the notebook and archived. Now I have to manually import that piece of data into my notebook page. Another aspect that we don’t have for budget reasons is the synchronization and access to a large commercial database of reagents. So we end up having to draw a lot of chemical structures ourselves. But it’s still very helpful, and once you are used to it, you cannot live without it.

Pamela Halpin obtained her PhD from Northern Illinois University and completed a post-doctoral fellowship with the FDA in Cincinnati. She has worked in R&D, analytical, and quality control labs, using a varied array of chemistriesn, from silicon at Dow Corning to complex inorganic pigments at Shepherd Color to surfactants and lubricants at BASF. She has been the Quality Operations Manager at the BASF production site in Cincinnati since 2010. This site has a variety of chemistries and methodologies that require both a depth and breadth of knowledge that makes for an interesting and fast-paced day.

Excerpts from an interview with Pamela Halpin, PhD, Quality Operations Manager at BASF.

Q: What drove your decision to transition to an ELN?

A: We are a central quality control (QC) laboratory, and the way we are set up is that we have our lab in one location but receive samples from two different locations. One set of samples comes from the building we are in and the other half come from our production plant across the river. We had no clear way to get the data from our lab to the production area. We were either faxing results from the instrument log or populating a spreadsheet and then calling people to tell them that the results were in. This was really cumbersome and the chemists in my group were functioning as transcription clerks. Sometimes there were errors in transcription and hence, we wanted the data to flow in an automated fashion to reduce the errors and get the chemists working as chemists, and not as clerks. This journey to acquire an ELN started in the fourth quarter of 2010, while we were still a part of Cognis Corporation. In 2011, we were purchased by BASF and we had to wait until our systems were integrated to figure out what we needed before we could make any changes.

Q: How did you determine what you needed in an ELN, in terms of its features and offerings?

A: We are a 24/7 operation with a team of nine chemists. I talked to all the chemists and asked them to identify their bottlenecks. Then I talked to the folks in production and asked them about issues that they were facing with the data. So I talked to all the people who were going to be using the ELN, from every aspect that it could be used, and developed our wants and needs based on that input. Essentially, we just wanted one system that would take the data from the instruments and put it where it needed to go. We wanted the ELN to perform certain calculations and access standard operating protocols (SOPs) and maintenance and calibration records and integrate with systems like SAP that we already had in place. We wanted the data to flow reliably and accurately and be located in one central system. Otherwise, the chemists would turn into electronic clerks.

Q: How did you go about picking the right vendor and product?

A: We picked a system that was a one-stop shop and integrated nicely with the systems we already had, to provide the connectivity that we needed. We first determined our wants and needs. For our needs, we drew a line in the sand and essentially eliminated all the vendors who couldn’t provide that. We then had three vendors come and demonstrate what they could offer. One of the things that I wanted was to be able to make changes on the fly, as is the case in a QC lab. Only one of the vendors could show us how to do that. We did a pilot run in November 2012, which was wildly successful; we then purchased the system in April of this year. For the pilot, we took data from one of our gas chromatography instruments and put it into a worksheet. We then had the ELN perform all the necessary calculations and we could check all the calibrations and inventory and access all the SOPs. The system is very user-friendly and fairly configurable. When we didn’t like the way it was initially set up, the vendor changed it and they were able to show us how to make the changes ourselves. We now can get all types of data-training data, calibration data, and such, so much faster than we previously could. We can also search the data by date, batch, instrument, or technique. We are planning to kick off our implementation project during the second week of June.

Q: What advice would you offer to people evaluating and implementing ELNs?

A: You really need to talk to all the people who are going to be using the system and put together a clear list of needs and wants. When you go out and talk to vendors, definitely have a script detailing what you want them to demonstrate, so you can compare apples to apples. If you have a clear list and a script ready, then you can make a very good decision. Once you have made your selection, you need to be in constant communication with the vendor. I would also recommend doing a pilot project, so you can find out more about the vendor’s customer service and the flexibility of the ELN.

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